In order to explore the effects of different malts on the flavor of beer after fermentation, the differences between 5 barley malts and 5 wheat malts on beer composition were analyzed by using metabolomics methods. The effects of different malts on the metabolic pathway of Saccharomyces cerevisiae during beer fermentation were explained at the metabolic level. After liquid chromatography-mass spectrometry (LC-MS) detection, principal component analysis (PCA) and orthogonal partial least squares discriminant analysis were performed to screen out the key metabolites that had the greatest impact on beer flavor. After linking the key metabolites to the flavor of beer, pathway enrichment was carried out. The results determined that barley malt mainly affects Purine metabolism, Pyrimidine metabolism, Arginine and proline metabolism, Alanine, aspartic acid and glutamate metabolism, Arginine biosynthesis, β-Alanine metabolism, Nicotinate and nicotinamide metabolism, Galactose metabolism and other pathways. Wheat malt mainly affects Purine metabolism, Pyrimidine metabolism, Arginine and proline metabolism, and Glutathione metabolism. These metabolic pathways have a key impact on the flavor of beer, which provides some theoretical guidance for the regulation of flavor substances in beer.